rs9508456

Variant names:

• chr13-29442225-C-T
• rs9508456
• NM_001033602.4:c.3184+2176C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033602.4(MTUS2):​c.3184+2176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,040 control chromosomes in the GnomAD database, including 7,957 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7957 hom., cov: 32)
• Consequence: MTUS2 NM_001033602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 1 publications found

Genes affected

MTUS2 (HGNC:20595): (microtubule associated scaffold protein 2) Enables microtubule binding activity and protein homodimerization activity. Part of nucleus. Colocalizes with centrosome and cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033602.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	NM_001033602.4	MANE Select	c.3184+2176C>T		intron	N/A	NP_001028774.3	Q5JR59-2
	MTUS2	NM_001384605.1		c.3184+2176C>T		intron	N/A	NP_001371534.1	Q5JR59-2
	MTUS2	NM_001384606.1		c.3184+2176C>T		intron	N/A	NP_001371535.1	Q5JR59-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS2	ENST00000612955.6	TSL:5 MANE Select	c.3184+2176C>T		intron	N/A	ENSP00000483729.2	Q5JR59-2
	MTUS2	ENST00000380808.6	TSL:1	c.121+2176C>T		intron	N/A	ENSP00000370186.2	Q5JR59-3
	MTUS2	ENST00000542829.1	TSL:1	c.-150+13329C>T		intron	N/A	ENSP00000445403.1	Q5JR59-4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45531 AN: 151922 Hom.: 7955 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.351

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.299 AC: 45530 AN: 152040 Hom.: 7957 Cov.: 32 AF XY: 0.296 AC XY: 22010 AN XY: 74294

African (AFR) AF: 0.121 AC: 5028 AN: 41482

American (AMR) AF: 0.342 AC: 5231 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3472

East Asian (EAS) AF: 0.201 AC: 1037 AN: 5162

South Asian (SAS) AF: 0.339 AC: 1636 AN: 4822

European-Finnish (FIN) AF: 0.271 AC: 2867 AN: 10562

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26634 AN: 67948

Other (OTH) AF: 0.348 AC: 734 AN: 2108

Alfa AF: 0.371 Hom.: 20777

Bravo AF: 0.296

Asia WGS AF: 0.264 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.56
PhyloP100		0.037
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9508456; hg19: chr13-30016362;